Dear Angel, Hi
If you want some helps about script and syntax for running this software it is in the README file of the program and is as below, hope that helps:
Program: MIREAP (Reap miRNAs from deeply sequenced smRNA library) Version: 0.2 Contact: Li Qibin firstname.lastname@example.org Bioinformatics department, Beijing Genomics Institute
1. Introduction MIREAP combines small RNA position and depth with a model of microRNA biogenesis to discover microRNAs from deeply sequenced small RNA library.
2. Installation You must have Vienna RNA Package (http://www.tbi.univie.ac.at/RNA) installed on your computer and make sure that its perl interface is accessible.
Copy mireap_0.2.tar.gz to a directory (/foo/bar) and unpack it by command: tar -zxvf mireap_0.2.tar.gz
Before running mireap, you need add path /foo/bar/mireap_0.1/lib to environment variable PERL5LIB: For csh/tcsh: setenv PERL5LIB /foo/bar/mireap_0.2/lib For sh/ksh/bash: export PERL5LIB=/foo/bar/mireap_0.2/lib
mireap.pl -i <smrna.fa> -m <map.txt> -r <reference.fa> -o <outdir>
-i <file> Small RNA library, fasta format, forced
-m <file> Mapping file, tabular format, forced
-r <file> Reference file, fasta format, forced
-o <dir> Directory where results produce (current directory)
-t <str> Sample label (xxx)
-A <int> Minimal miRNA sequence length (18)
-B <int> Maximal miRNA sequence length (26)
-a <int> Minimal miRNA reference sequence length (20)
-b <int> Maximal miRNA reference sequence length (24)
-u <int> Maximal copy number of miRNAs on reference (20)
-e <folat> Maximal free energy allowed for a miRNA precursor (-18)
-d <int> Maximal space between miRNA and miRNA* (35)
-p <int> Minimal base pairs of miRNA and miRNA*
-v <int> Maximal bulge of miRNA and miRNA* (4)
-s <int> Maximal asymmetry of miRNA/miRNA* duplex
-f <int> Flank sequence length of miRNA precursor (10)
Please convert your small RNA file into fasta format and append sequencing frequence to sequence Id, just like this entry:
t0000035 3234 GAATGGATAAGGATTAGCGATGATACA (t0000035 is read_ID, 3234 is sequencing frequence)
The format of small RNA mapping file should be (delimited by tab or space): read_ID,chr_ID,start,end,strand(+/-)
You can make MIREAP run on the test data by execute comand: perl ../bin/mireap.pl -i rna.fa -m map.txt -r ref.fa .
4. Output format MIREAP produce three files at each run.
*.gff This file contains miRNA genes discovered by MIREAP, GFF3 format. For GFF3 format, please refer to http://www.sequenceontology.org/gff3.shtml Attribute 'Count' denotes the sequenceing frequence.
*.aln This file contains sequence and structure of the pre-miRNA. Small RNAs also are aligned to the precursor from which you can get more insights into the maturation process of miRNAs.
*.log This log file records parameters, start end time and other informations.